The Role of Protein Engineering in Biomedical Applications of Mammalian Synthetic Biology

Bojar, Daniel; Fussenegger, Martin

doi:10.1002/smll.201903093

Cited by 16 publications

(8 citation statements)

References 104 publications

(109 reference statements)

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“…A series of chimera samples, including mIFP‐K72 and GFP‐K72, and other polypeptides, including K18 and K36 for control experiments, were designed and prepared (preparation details are given in Supporting Information, Figures S1 and S2 and Table S1, Supporting Information). [ 33,34 ] All proteins were characterized by both polyacrylamide gel electrophoresis and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry, respectively (Figures S3 and S4, Supporting Information). The anionic polyelectrolyte component is a biocompatible carboxylated polyethylene glycol (PEG‐COO − ) (Figure S5, Supporting Information).…”

Section: Figurementioning

confidence: 99%

Engineered Near‐Infrared Fluorescent Protein Assemblies for Robust Bioimaging and Therapeutic Applications

Sun

et al. 2020

Advanced Materials

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Near-infrared (NIR) fluorescence imaging is an evolving field enabling high-resolution imaging and diagnosis in biomedicine. Due to the reduced photon scattering and minimal tissue absorption, fluorescence imaging in the NIR window Fluorescent proteins are investigated extensively as markers for the imaging of cells and tissues that are treated by gene transfection. However, limited transfection efficiency and lack of targeting restrict the clinical application of this method rooted in the challenging development of robust fluorescent proteins for in vivo bioimaging. To address this, a new type of near-infrared (NIR) fluorescent protein assemblies manufactured by genetic engineering is presented. Due to the formation of well-defined nanoparticles and spectral operation within the phototherapeutic window, the NIR protein aggregates allow stable and specific tumor imaging via simple exogenous injection. Importantly, in vivo tumor metastases are tracked and this overcomes the limitations of in vivo imaging that can only be implemented relying on the gene transfection of fluorescent proteins. Concomitantly, the efficient loading of hydrophobic drugs into the protein nanoparticles is demonstrated facilitating the therapy of tumors in a mouse model. It is believed that these theranostic NIR fluorescent protein assemblies, hence, show great potential for the in vivo detection and therapy of cancer.(700-1700 nm) offers increased tissue penetration depths and a better signal-to-noise ratio rendering it ideal for biomedical applications. [1][2][3][4][5][6][7] Currently, NIR fluorescent materials mainly comprise quantum dots, [8][9][10] lanthanide-doped upconverting nanoparticles, [11][12][13] organic small molecules, [14,15] and polymer-based systems. [16] However, long-term toxicity and immunogenicity, non-biodegradability, as well as photo-instability of these non-life-like materials have restricted their translation into clinical applications. [17][18][19][20][21][22] Thus, the development of new fluorophores with increased biocompatibility and biosafety as imaging diagnostic tools is essential for biomedical application.Fluorescent proteins (FPs), such as redshifted fluorescent protein and engineered monomeric near-infrared fluorescent proteins (mIFPs), were proven to be excellent candidates for noninvasive labeling and whole-body imaging in living organisms due to the low light scattering/background noise, reduced autofluorescence, and relatively easy construction procedure. [23][24][25][26][27][28][29][30] Typically, those fluorophores are genetically encoded and must be produced by gene transfection into living cells and animals for bioimaging. However, the transfection efficiency is limited and the FPs expressed by this procedure are unable to target tumors effectively owing to the lack of specific binding sites. [31,32] Moreover, FPs that are expressed by hosts such as Escherichia coli and yeast are rarely reported for direct in vivo bioimaging. This most likely stems from the fast photobleaching in blood protease...

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Section: Figurementioning

confidence: 99%

Engineered Near‐Infrared Fluorescent Protein Assemblies for Robust Bioimaging and Therapeutic Applications

Sun

et al. 2020

Advanced Materials

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“…Protein engineering is an important tool in synthetic biology that can produce proteins with incredible therapeutic and industrial potential (Tobin et al, 2015;Chica, 2015;Bojar and Fussenegger, 2020). In recent years, the field has made giant strides forward, but it still has the potential for exponential growth -as seen for many fields that benefit from high throughput technologies and powerful new computational tools.…”

Section: Introductionmentioning

confidence: 99%

Surfaces: A software to quantify and visualize interactions within and between proteins and ligands

Teruel

Borges

Najmanovich

2023

Preprint

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Computational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and complexes are fundamental to understand, modulate and engineer biological processes. Here we present Surfaces, an easy to use, fast and customizable software for quantification and visualization of molecular interactions based on the calculation of surface areas in contact. Surfaces calculations shows equivalent levels of correlations with experimental data as computationally expensive methods based on molecular dynamics. All scripts are available at https://github.com/nataliateruel/Surfaces

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“…Protein engineering is an important tool in biotechnology that can produce proteins with improved therapeutic and industrial profiles ( Chica 2015 , Tobin et al 2015 , Bojar and Fussenegger 2020 ). In recent years, the field has made giant strides forward, but it still has the potential for exponential growth—as seen for many fields that benefit from high-throughput technologies and powerful new computational tools.…”

Section: Introductionmentioning

confidence: 99%

Surfaces: a software to quantify and visualize interactions within and between proteins and ligands

Teruel,

Borges,

Najmanovich

2023

Bioinformatics

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Summary Computational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and complexes are fundamental to understand, modulate and engineer biological processes. Here, we present Surfaces, an easy to use, fast and customizable software for quantification and visualization of molecular interactions based on the calculation of surface areas in contact. Surfaces calculations shows equivalent or better correlations with experimental data as computationally expensive methods based on molecular dynamics. Availability and implementation All scripts are available at https://github.com/NRGLab/Surfaces. Surface’s documentation is available at https://surfaces-tutorial.readthedocs.io/en/latest/index.html.

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The Role of Protein Engineering in Biomedical Applications of Mammalian Synthetic Biology

Cited by 16 publications

References 104 publications

Engineered Near‐Infrared Fluorescent Protein Assemblies for Robust Bioimaging and Therapeutic Applications

Engineered Near‐Infrared Fluorescent Protein Assemblies for Robust Bioimaging and Therapeutic Applications

Surfaces: A software to quantify and visualize interactions within and between proteins and ligands

Surfaces: a software to quantify and visualize interactions within and between proteins and ligands

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